@jcode.labs/ragmir 6.3.1 → 6.5.0

package/README.md

@@ -11,8 +11,8 @@
 </p>
 
 <p align="center">
-  93% of real developer questions find the right file in the top 10 · 40 ms median search on a
-  43,874-chunk monorepo · <a href="https://github.com/jcode-works/jcode-ragmir#benchmarks">benchmarks</a>
+  94% of real developer questions find the right file in the top 10 · 36 ms median search on a
+  30,171-chunk monorepo · <a href="https://github.com/jcode-works/jcode-ragmir#benchmarks">benchmarks</a>
 </p>
 
 <p align="center">
@@ -31,12 +31,14 @@ model you choose. Ragmir does not bundle a chat model or host your documents.
 
 - **Code and documents in one index:** hybrid BM25 and vector search that understands paths and
   camelCase identifiers and boosts the code that defines what you ask about.
-- **Fast on real repositories:** 40 ms median search on a 43,874-chunk monorepo, with the right
-  source in the top 10 for 93% of real developer questions
+- **Fast on real repositories:** 36 ms median search on a 30,171-chunk monorepo, with the right
+  source in the top 10 for 94% of real developer questions
   ([benchmarks](https://github.com/jcode-works/jcode-ragmir#benchmarks)).
+- **Ahead of the usual RAG stacks:** the right file reaches the top 3 for 83% of this repository's
+  developer questions, against 63% for a LangChain.js pipeline and 79% for MiniSearch BM25.
 - **Evidence you can verify:** citations point to source lines or native page, slide, sheet/cell,
   and EPUB coordinates. Results flag changed files (`sourceStatus`) and thin support
-  (`weakEvidence`); unrelated questions return nothing.
+  (`weakEvidence`); questions your sources cannot answer return nothing instead of noise.
 - **Always current:** `rgr doctor` checks the files on disk on every run, and `rgr hooks install`
   refreshes the index after commits, merges, and checkouts.
 - **Private and portable:** offline by default, with no account or telemetry, and the same paths,
@@ -111,7 +113,10 @@ scripts. See the [API reference](https://github.com/jcode-works/jcode-ragmir/blo
 Index Markdown, code, JSON, CSV, HTML, PDF, DOCX, XLSX, PPTX, OpenDocument, EPUB, and RTF; scanned
 PDFs, photos, and legacy `.doc` files use local extractors (`rgr ocr setup --images
 --legacy-word`). The default `local-hash` provider needs no model download. For semantic
-embeddings, install `@huggingface/transformers` and run `npx rgr setup --semantic`.
+embeddings, install `@huggingface/transformers` and run `npx rgr setup --semantic`. Use
+`mxbai-embed-xsmall-v1` for English, `multilingual-e5-small` (the default) or `multilingual-e5-base`
+for French and mixed languages; newer models such as Granite R2 or EmbeddingGemma 2 are not
+supported yet. See [choosing an embedding model](https://github.com/jcode-works/jcode-ragmir#choosing-an-embedding-model).
 
 For guided setup, give your agent this prompt:
 

package/dist/abstention-calibration.d.ts

@@ -0,0 +1,29 @@
+import type { Table } from "@lancedb/lancedb";
+import type { AbstentionCalibration, Config, IndexManifest } from "./types.js";
+/**
+ * Off-topic questions in English, French, and nonsense, chosen to share no subject with a software
+ * project. Their nearest passages mark where unrelated questions land in an index, whatever the
+ * embedding model. Changing the list changes every calibration, so keep it stable.
+ */
+export declare const ABSTENTION_PROBES: readonly string[];
+/** The embedding function, `embedTexts` in production, so callers pass it without a wrapper. */
+export type ProbeEmbedder = (texts: string[], config: Config, inputType: "query", signal?: AbortSignal) => Promise<number[][]>;
+/**
+ * Measure the noise floor of an index: embed the probes as queries and take the smallest exact
+ * distance to their nearest passage. Returns null for local-hash indexes and empty tables.
+ */
+export declare function measureAbstentionCalibration(table: Table, config: Config, embed: ProbeEmbedder, signal?: AbortSignal): Promise<AbstentionCalibration | null>;
+/**
+ * The noise floor search applies: stored by ingestion, or measured once per process and index
+ * generation for an index built before ingestion stored it. A failed measurement keeps the
+ * policy's own distances.
+ */
+export declare function indexNoiseFloor(table: Table, config: Config, manifest: IndexManifest | null, generationKey: string, embed: ProbeEmbedder): Promise<number | null>;
+/**
+ * Advice for a semantic index built before ingestion stored its noise floor: every process then
+ * measures it on its first search, which cost 0.1 to 0.3 s on real bases.
+ */
+export declare function noiseFloorAdvice(manifest: IndexManifest | null, config: Config, run: (args: string[]) => string): string | null;
+/** The calibration stored with the index, when it was measured with the configured model. */
+export declare function manifestNoiseFloor(manifest: IndexManifest | null, config: Config): number | null;
+//# sourceMappingURL=abstention-calibration.d.ts.map

package/dist/abstention-calibration.d.ts.map

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package/dist/abstention-calibration.js

@@ -0,0 +1,116 @@
+/**
+ * Off-topic questions in English, French, and nonsense, chosen to share no subject with a software
+ * project. Their nearest passages mark where unrelated questions land in an index, whatever the
+ * embedding model. Changing the list changes every calibration, so keep it stable.
+ */
+export const ABSTENTION_PROBES = [
+    "Who won the Super Bowl in 1998?",
+    "How long should I boil an egg?",
+    "What is the population of Canada?",
+    "Best beaches in Portugal for surfing",
+    "How to knit a scarf for beginners",
+    "What time is sunset in Tokyo today?",
+    "Who were the members of the Beatles?",
+    "How do volcanoes form?",
+    "Recommend a good fantasy novel",
+    "What is the exchange rate of the euro to the yen?",
+    "Quelle est la capitale de l'Argentine ?",
+    "Comment préparer une pâte à crêpes ?",
+    "Qui a gagné Roland-Garros en 2015 ?",
+    "Quel temps fera-t-il à Nice demain ?",
+    "Comment entretenir un aquarium d'eau douce ?",
+    "Quelle est la distance entre la Terre et la Lune ?",
+    "Quels sont les meilleurs vins de Bourgogne ?",
+    "Comment apprendre à jouer de la guitare ?",
+    "flimbo grastic wuvvle",
+    "trepax zondor kliffum",
+    "asdkj qwpoe zmxn",
+    "lorem quantum frabble",
+    "Combien de temps vit un chat domestique ?",
+    "What is the tallest mountain in Africa?",
+];
+const MAX_MEASURED_FLOORS = 4;
+// Noise floors measured at search time for indexes built before ingestion stored one.
+const measuredFloors = new Map();
+/**
+ * Measure the noise floor of an index: embed the probes as queries and take the smallest exact
+ * distance to their nearest passage. Returns null for local-hash indexes and empty tables.
+ */
+export async function measureAbstentionCalibration(table, config, embed, signal) {
+    if (config.embeddingProvider !== "transformers") {
+        return null;
+    }
+    const vectors = await embed([...ABSTENTION_PROBES], config, "query", signal);
+    const distances = [];
+    for (const vector of vectors) {
+        const [nearest] = await table
+            .vectorSearch(vector)
+            .bypassVectorIndex()
+            .select(["id"])
+            .limit(1)
+            .toArray();
+        if (typeof nearest?._distance === "number" && Number.isFinite(nearest._distance)) {
+            distances.push(nearest._distance);
+        }
+    }
+    if (distances.length === 0) {
+        return null;
+    }
+    return {
+        schemaVersion: 1,
+        embeddingModel: config.embeddingModel,
+        probeCount: distances.length,
+        noiseFloorDistance: Math.min(...distances),
+    };
+}
+/**
+ * The noise floor search applies: stored by ingestion, or measured once per process and index
+ * generation for an index built before ingestion stored it. A failed measurement keeps the
+ * policy's own distances.
+ */
+export function indexNoiseFloor(table, config, manifest, generationKey, embed) {
+    if (config.embeddingProvider !== "transformers" || !manifest?.chunkCount) {
+        return Promise.resolve(null);
+    }
+    const stored = manifestNoiseFloor(manifest, config);
+    if (stored !== null) {
+        return Promise.resolve(stored);
+    }
+    const cacheKey = `${generationKey}\0${config.embeddingModel}`;
+    let measured = measuredFloors.get(cacheKey);
+    if (!measured) {
+        measured = measureAbstentionCalibration(table, config, embed)
+            .then((calibration) => calibration?.noiseFloorDistance ?? null)
+            .catch(() => null);
+        measuredFloors.set(cacheKey, measured);
+        for (const key of measuredFloors.keys()) {
+            if (measuredFloors.size <= MAX_MEASURED_FLOORS)
+                break;
+            measuredFloors.delete(key);
+        }
+    }
+    return measured;
+}
+/**
+ * Advice for a semantic index built before ingestion stored its noise floor: every process then
+ * measures it on its first search, which cost 0.1 to 0.3 s on real bases.
+ */
+export function noiseFloorAdvice(manifest, config, run) {
+    if (config.embeddingProvider !== "transformers" ||
+        !manifest?.chunkCount ||
+        manifestNoiseFloor(manifest, config) !== null) {
+        return null;
+    }
+    return `The index has no stored noise floor, so each process measures it on its first search. Run \`${run(["ingest"])}\` to store it.`;
+}
+/** The calibration stored with the index, when it was measured with the configured model. */
+export function manifestNoiseFloor(manifest, config) {
+    const calibration = manifest?.abstentionCalibration;
+    if (config.embeddingProvider !== "transformers" ||
+        calibration?.schemaVersion !== 1 ||
+        calibration.embeddingModel !== config.embeddingModel) {
+        return null;
+    }
+    return calibration.noiseFloorDistance;
+}
+//# sourceMappingURL=abstention-calibration.js.map

package/dist/abstention-calibration.js.map

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package/dist/chunk-stats.d.ts.map

@@ -1 +1 @@
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package/dist/chunk-stats.js

@@ -1,3 +1,4 @@
+import { percentile } from "./statistics.js";
 export function summarizeChunkStats(chunks) {
     if (chunks.length === 0) {
         return {
@@ -24,8 +25,4 @@ export function summarizeChunkStats(chunks) {
         contextualRatio: contextualChunks / chunks.length,
     };
 }
-function percentile(sortedValues, quantile) {
-    const index = Math.ceil(quantile * sortedValues.length) - 1;
-    return sortedValues[Math.max(0, index)] ?? 0;
-}
 //# sourceMappingURL=chunk-stats.js.map

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@@ -1 +1 @@
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+{"version":3,"file":"chunk-stats.js","sourceRoot":"","sources":["../src/chunk-stats.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAA;AAQ5C,MAAM,UAAU,mBAAmB,CAAC,MAA6B;IAC/D,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO;YACL,KAAK,EAAE,CAAC;YACR,QAAQ,EAAE,CAAC;YACX,YAAY,EAAE,CAAC;YACf,QAAQ,EAAE,CAAC;YACX,QAAQ,EAAE,CAAC;YACX,QAAQ,EAAE,CAAC;YACX,gBAAgB,EAAE,CAAC;YACnB,eAAe,EAAE,CAAC;SACnB,CAAA;IACH,CAAC;IAED,MAAM,OAAO,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC,IAAI,GAAG,KAAK,CAAC,CAAA;IAC5F,MAAM,gBAAgB,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,MAAM,CAAA;IAE7F,OAAO;QACL,KAAK,EAAE,MAAM,CAAC,MAAM;QACpB,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC;QACzB,YAAY,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,CAAC,GAAG,GAAG,MAAM,EAAE,CAAC,CAAC,GAAG,OAAO,CAAC,MAAM;QAC/E,QAAQ,EAAE,UAAU,CAAC,OAAO,EAAE,GAAG,CAAC;QAClC,QAAQ,EAAE,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC;QACnC,QAAQ,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QAC7B,gBAAgB;QAChB,eAAe,EAAE,gBAAgB,GAAG,MAAM,CAAC,MAAM;KAClD,CAAA;AACH,CAAC"}

package/dist/config.d.ts

@@ -4,7 +4,6 @@ export interface ConfigLoadDiagnosticsEvent {
     projectRoot: string;
     configPath: string;
 }
-export declare const RETIRED_CONFIG_KEYS: readonly ["privacyProfile", "acceptedRisks", "redaction", "accessLog", "accessLogPath"];
 export declare function retiredConfigKeys(raw: Record<string, unknown>): string[];
 export interface ProjectConfigFile {
     projectRoot: string;
@@ -24,11 +23,6 @@ export declare function projectConfigExists(location: ProjectConfigFile): boolea
 export declare function readMergedProjectConfig(location: ProjectConfigFile): Promise<Record<string, unknown>>;
 export declare function loadConfig(start?: string): Promise<Config>;
 export declare function externalExtractorsRequested(config: Config): boolean;
-/** Budgets each retrieval profile chooses for fields the config leaves unset. */
-export declare const RETRIEVAL_PROFILE_BUDGETS: Readonly<Record<Exclude<Config["retrievalProfile"], "custom">, {
-    topK: number;
-    hybridTextScanLimit: number;
-}>>;
 /**
  * Budgets pinned in the config that differ from the selected profile. Older `rgr init` wrote every
  * default, so a later switch to the quality profile silently kept topK 8.

package/dist/config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAmCA,OAAO,KAAK,EAAE,MAAM,EAAiB,MAAM,YAAY,CAAA;AAEvD,eAAO,MAAM,+BAA+B,uBAAuB,CAAA;AAEnE,MAAM,WAAW,0BAA0B;IACzC,WAAW,EAAE,MAAM,CAAA;IACnB,UAAU,EAAE,MAAM,CAAA;CACnB;AA8JD,eAAO,MAAM,mBAAmB,YAC9B,gBAAgB,EAChB,eAAe,EACf,WAAW,EACX,WAAW,EACX,eAAe,CACP,CAAA;AAEV,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAExE;AAED,MAAM,WAAW,iBAAiB;IAChC,WAAW,EAAE,MAAM,CAAA;IACnB,0FAA0F;IAC1F,UAAU,EAAE,MAAM,CAAA;IAClB,6FAA6F;IAC7F,eAAe,EAAE,MAAM,CAAA;IACvB,gEAAgE;IAChE,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAA;IAC/B,MAAM,EAAE,OAAO,CAAA;CAChB;AAED,wBAAgB,eAAe,CAAC,KAAK,SAAgB,GAAG,MAAM,CAE7D;AAED,wBAAgB,iBAAiB,CAAC,KAAK,SAAgB,GAAG,iBAAiB,CA2C1E;AAED,oEAAoE;AACpE,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,iBAAiB,GAAG,OAAO,CAExE;AAED,4FAA4F;AAC5F,wBAAsB,uBAAuB,CAC3C,QAAQ,EAAE,iBAAiB,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAQlC;AAaD,wBAAsB,UAAU,CAAC,KAAK,SAAgB,GAAG,OAAO,CAAC,MAAM,CAAC,CA6FvE;AAED,wBAAgB,2BAA2B,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAEnE;AA0CD,iFAAiF;AACjF,eAAO,MAAM,yBAAyB,EAAE,QAAQ,CAC9C,MAAM,CACJ,OAAO,CAAC,MAAM,CAAC,kBAAkB,CAAC,EAAE,QAAQ,CAAC,EAC7C;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,mBAAmB,EAAE,MAAM,CAAA;CAAE,CAC9C,CAQF,CAAA;AAiBD;;;GAGG;AACH,wBAAgB,yBAAyB,CACvC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC5B,OAAO,EAAE,MAAM,CAAC,kBAAkB,CAAC,GAClC,KAAK,CAAC;IAAE,KAAK,EAAE,MAAM,GAAG,qBAAqB,CAAC;IAAC,UAAU,EAAE,MAAM,CAAC;IAAC,YAAY,EAAE,MAAM,CAAA;CAAE,CAAC,CAW5F"}
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAoCA,OAAO,KAAK,EAAE,MAAM,EAAiB,MAAM,YAAY,CAAA;AAEvD,eAAO,MAAM,+BAA+B,uBAAuB,CAAA;AAEnE,MAAM,WAAW,0BAA0B;IACzC,WAAW,EAAE,MAAM,CAAA;IACnB,UAAU,EAAE,MAAM,CAAA;CACnB;AA0KD,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAExE;AAED,MAAM,WAAW,iBAAiB;IAChC,WAAW,EAAE,MAAM,CAAA;IACnB,0FAA0F;IAC1F,UAAU,EAAE,MAAM,CAAA;IAClB,6FAA6F;IAC7F,eAAe,EAAE,MAAM,CAAA;IACvB,gEAAgE;IAChE,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAA;IAC/B,MAAM,EAAE,OAAO,CAAA;CAChB;AAED,wBAAgB,eAAe,CAAC,KAAK,SAAgB,GAAG,MAAM,CAE7D;AAED,wBAAgB,iBAAiB,CAAC,KAAK,SAAgB,GAAG,iBAAiB,CA2C1E;AAED,oEAAoE;AACpE,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,iBAAiB,GAAG,OAAO,CAExE;AAED,4FAA4F;AAC5F,wBAAsB,uBAAuB,CAC3C,QAAQ,EAAE,iBAAiB,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAQlC;AAaD,wBAAsB,UAAU,CAAC,KAAK,SAAgB,GAAG,OAAO,CAAC,MAAM,CAAC,CAiGvE;AAED,wBAAgB,2BAA2B,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAEnE;AAwED;;;GAGG;AACH,wBAAgB,yBAAyB,CACvC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC5B,OAAO,EAAE,MAAM,CAAC,kBAAkB,CAAC,GAClC,KAAK,CAAC;IAAE,KAAK,EAAE,MAAM,GAAG,qBAAqB,CAAC;IAAC,UAAU,EAAE,MAAM,CAAC;IAAC,YAAY,EAAE,MAAM,CAAA;CAAE,CAAC,CAW5F"}

package/dist/config.js

@@ -4,6 +4,7 @@ import { readFile } from "node:fs/promises";
 import path from "node:path";
 import { z } from "zod";
 import { CONFIG_PATH, DEFAULT_CONFIG, defaultEmbeddingModelRevision, LEGACY_CONFIG_PATH, LEGACY_DEFAULT_CONFIG, MAX_CHUNK_SIZE, MAX_CHUNKS_PER_DOCUMENT, MAX_CONFIG_ARRAY_ITEMS, MAX_CONFIG_NAME_CHARACTERS, MAX_CONFIG_PATH_CHARACTERS, MAX_CONFIG_TEXT_CHARACTERS, MAX_CONFIGURED_FILE_BYTES, MAX_EMBEDDING_BATCH_SIZE, MAX_EXTERNAL_COMMAND_ARGUMENTS, MAX_EXTERNAL_COMMAND_TIMEOUT_MS, MAX_HYBRID_TEXT_SCAN_LIMIT, MAX_INCLUDE_EXTENSIONS, MAX_INGEST_CHUNKS_PER_FILE, MAX_INGEST_CONCURRENCY, MAX_MCP_OUTPUT_BYTES, MAX_SEARCH_SCOPES, MAX_SEARCH_TOP_K, MAX_SOURCE_WEIGHT, MAX_WORKLOAD_CONCURRENCY, MAX_WORKLOAD_QUEUE, MAX_WORKLOAD_QUEUE_TIMEOUT_MS, SHARED_CONFIG_FILENAME, } from "./defaults.js";
+import { RagmirError } from "./errors.js";
 import { isRecord } from "./guards.js";
 export const CONFIG_LOAD_DIAGNOSTICS_CHANNEL = "ragmir:config-load";
 const configLoadDiagnostics = channel(CONFIG_LOAD_DIAGNOSTICS_CHANNEL);
@@ -14,6 +15,7 @@ const embeddingModelDigestSchema = z
     .nullable();
 const retrievalProfileSchema = z.enum(["fast", "balanced", "quality", "custom"]);
 const sourceFingerprintModeSchema = z.enum(["fast", "strict"]);
+const ingestEmbeddingDeviceSchema = z.enum(["cpu", "webgpu"]);
 const incrementalFailurePolicySchema = z.enum(["preserve-last-good", "remove-stale"]);
 const configPathSchema = z.string().min(1).max(MAX_CONFIG_PATH_CHARACTERS);
 const configTextSchema = z.string().min(1).max(MAX_CONFIG_TEXT_CHARACTERS);
@@ -85,6 +87,7 @@ const rawConfigSchema = z
     maxFileBytes: z.number().int().positive().default(DEFAULT_CONFIG.maxFileBytes),
     ingestConcurrency: z.number().int().positive().default(DEFAULT_CONFIG.ingestConcurrency),
     embeddingBatchSize: z.number().int().positive().default(DEFAULT_CONFIG.embeddingBatchSize),
+    ingestEmbeddingDevice: ingestEmbeddingDeviceSchema.default(DEFAULT_CONFIG.ingestEmbeddingDevice),
     sourceFingerprintMode: sourceFingerprintModeSchema.default(DEFAULT_CONFIG.sourceFingerprintMode),
     incrementalFailurePolicy: incrementalFailurePolicySchema.default(DEFAULT_CONFIG.incrementalFailurePolicy),
     hybridTextScanLimit: z.number().int().positive().default(DEFAULT_CONFIG.hybridTextScanLimit),
@@ -147,7 +150,7 @@ const rawConfigSchema = z
         .default(DEFAULT_CONFIG.mcpSeenResults),
 })
     .strict();
-export const RETIRED_CONFIG_KEYS = [
+const RETIRED_CONFIG_KEYS = [
     "privacyProfile",
     "acceptedRisks",
     "redaction",
@@ -227,7 +230,9 @@ export async function loadConfig(start = process.cwd()) {
     const raw = await readMergedProjectConfig(projectConfig);
     const retired = retiredConfigKeys(raw);
     if (retired.length > 0) {
-        throw new Error(`Retired configuration fields: ${retired.join(", ")}. Run \`rgr upgrade\` to back up and migrate the config and rebuild the index. Ragmir now preserves source text without masking; your consuming model controls where retrieved content is sent.`);
+        // A typed code lets agents and MCP clients route to `rgr upgrade` instead of reporting an
+        // internal failure.
+        throw new RagmirError("CONFIG_MIGRATION_REQUIRED", `Retired configuration fields: ${retired.join(", ")}. Run \`rgr upgrade\` to back up and migrate the config and rebuild the index. Ragmir now preserves source text without masking; your consuming model controls where retrieved content is sent.`);
     }
     const defaults = projectConfig.legacy ? LEGACY_DEFAULT_CONFIG : DEFAULT_CONFIG;
     const parsed = rawConfigSchema.parse(configWithModelIdentityDefaults(defaults, raw));
@@ -267,6 +272,7 @@ export async function loadConfig(start = process.cwd()) {
         maxFileBytes: effective.maxFileBytes,
         ingestConcurrency: effective.ingestConcurrency,
         embeddingBatchSize: effective.embeddingBatchSize,
+        ingestEmbeddingDevice: effective.ingestEmbeddingDevice,
         sourceFingerprintMode: effective.sourceFingerprintMode,
         incrementalFailurePolicy: effective.incrementalFailurePolicy,
         hybridTextScanLimit: effective.hybridTextScanLimit,
@@ -338,7 +344,7 @@ function configWithModelIdentityDefaults(defaults, raw) {
     };
 }
 /** Budgets each retrieval profile chooses for fields the config leaves unset. */
-export const RETRIEVAL_PROFILE_BUDGETS = {
+const RETRIEVAL_PROFILE_BUDGETS = {
     fast: { topK: 5, hybridTextScanLimit: 2_000 },
     balanced: {
         topK: DEFAULT_CONFIG.topK,

package/dist/config.js.map

@@ -1 +1 @@
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package/dist/defaults.d.ts

@@ -2,7 +2,6 @@ import type { Config } from "./types.js";
 export declare const RAGMIR_DIR = ".ragmir";
 export declare const LEGACY_KB_DIR = ".kb";
 export declare const LEGACY_PRIVATE_DIR = "private";
-export declare const RAGMIR_RAW_DIR = ".ragmir/raw";
 export declare const CONFIG_PATH = ".ragmir/config.json";
 /** Optional project-level config meant to be committed; `.ragmir/config.json` overrides its keys. */
 export declare const SHARED_CONFIG_FILENAME = "ragmir.config.json";
@@ -20,6 +19,7 @@ export declare const MAX_INGEST_CHUNK_WINDOW = 8192;
 export declare const MAX_INGEST_CHUNKS_PER_FILE = 65536;
 export declare const MAX_INGEST_VECTOR_BYTES_PER_FILE: number;
 export declare const MAX_SEARCH_TOP_K = 100;
+/** A document can fill at most one full result page. @alias */
 export declare const MAX_CHUNKS_PER_DOCUMENT = 100;
 export declare const MAX_HYBRID_TEXT_SCAN_LIMIT = 10000;
 export declare const MAX_CONFIG_ARRAY_ITEMS = 10000;
@@ -36,16 +36,12 @@ export declare const MAX_WORKLOAD_QUEUE_TIMEOUT_MS = 900000;
 export declare const MAX_CONFIG_NAME_CHARACTERS = 120;
 export declare const MAX_SOURCE_WEIGHT = 10;
 export declare const MAX_SEARCH_SCOPES = 64;
-export declare const DEFAULT_EMBEDDING_MODEL = "intfloat/multilingual-e5-small";
-export declare const DEFAULT_EMBEDDING_MODEL_REVISION = "614241f622f53c4eeff9890bdc4f31cfecc418b3";
-export declare const KNOWN_EMBEDDING_MODEL_REVISIONS: Readonly<Record<string, string>>;
 /** Budgets that `retrievalProfile` chooses unless a project config sets them explicitly. */
 export declare const RETRIEVAL_PROFILE_FIELDS: ReadonlySet<string>;
 export declare function defaultEmbeddingModelRevision(model: string): string;
 export declare const RAGMIR_GITIGNORE_ENTRY = ".ragmir/";
 export declare const LEGACY_KB_GITIGNORE_ENTRY = ".kb/";
 export declare const LEGACY_PRIVATE_GITIGNORE_ENTRY = "private/";
-export declare const LEGACY_PRIVATE_GITIGNORE_FALLBACK_ENTRY = "private/**";
 export declare const DEFAULT_CONFIG: Omit<Config, "projectRoot">;
 export declare const LEGACY_DEFAULT_CONFIG: Omit<Config, "projectRoot">;
 //# sourceMappingURL=defaults.d.ts.map

package/dist/defaults.d.ts.map

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package/dist/defaults.js

@@ -1,7 +1,7 @@
 export const RAGMIR_DIR = ".ragmir";
 export const LEGACY_KB_DIR = ".kb";
 export const LEGACY_PRIVATE_DIR = "private";
-export const RAGMIR_RAW_DIR = `${RAGMIR_DIR}/raw`;
+const RAGMIR_RAW_DIR = `${RAGMIR_DIR}/raw`;
 export const CONFIG_PATH = `${RAGMIR_DIR}/config.json`;
 /** Optional project-level config meant to be committed; `.ragmir/config.json` overrides its keys. */
 export const SHARED_CONFIG_FILENAME = "ragmir.config.json";
@@ -19,6 +19,7 @@ export const MAX_INGEST_CHUNK_WINDOW = 8_192;
 export const MAX_INGEST_CHUNKS_PER_FILE = 65_536;
 export const MAX_INGEST_VECTOR_BYTES_PER_FILE = 256 * 1_024 * 1_024;
 export const MAX_SEARCH_TOP_K = 100;
+/** A document can fill at most one full result page. @alias */
 export const MAX_CHUNKS_PER_DOCUMENT = MAX_SEARCH_TOP_K;
 export const MAX_HYBRID_TEXT_SCAN_LIMIT = 10_000;
 export const MAX_CONFIG_ARRAY_ITEMS = 10_000;
@@ -35,9 +36,9 @@ export const MAX_WORKLOAD_QUEUE_TIMEOUT_MS = 900_000;
 export const MAX_CONFIG_NAME_CHARACTERS = 120;
 export const MAX_SOURCE_WEIGHT = 10;
 export const MAX_SEARCH_SCOPES = 64;
-export const DEFAULT_EMBEDDING_MODEL = "intfloat/multilingual-e5-small";
-export const DEFAULT_EMBEDDING_MODEL_REVISION = "614241f622f53c4eeff9890bdc4f31cfecc418b3";
-export const KNOWN_EMBEDDING_MODEL_REVISIONS = {
+const DEFAULT_EMBEDDING_MODEL = "intfloat/multilingual-e5-small";
+const DEFAULT_EMBEDDING_MODEL_REVISION = "614241f622f53c4eeff9890bdc4f31cfecc418b3";
+const KNOWN_EMBEDDING_MODEL_REVISIONS = {
     [DEFAULT_EMBEDDING_MODEL]: DEFAULT_EMBEDDING_MODEL_REVISION,
     "mixedbread-ai/mxbai-embed-xsmall-v1": "e6ac24e5d6efb8782b59de1647b3ececb4ece94e",
 };
@@ -52,7 +53,6 @@ export function defaultEmbeddingModelRevision(model) {
 export const RAGMIR_GITIGNORE_ENTRY = `${RAGMIR_DIR}/`;
 export const LEGACY_KB_GITIGNORE_ENTRY = `${LEGACY_KB_DIR}/`;
 export const LEGACY_PRIVATE_GITIGNORE_ENTRY = `${LEGACY_PRIVATE_DIR}/`;
-export const LEGACY_PRIVATE_GITIGNORE_FALLBACK_ENTRY = `${LEGACY_PRIVATE_DIR}/**`;
 export const DEFAULT_CONFIG = {
     retrievalProfile: "balanced",
     rawDir: RAGMIR_RAW_DIR,
@@ -75,6 +75,7 @@ export const DEFAULT_CONFIG = {
     maxFileBytes: 50_000_000,
     ingestConcurrency: 4,
     embeddingBatchSize: 32,
+    ingestEmbeddingDevice: "cpu",
     sourceFingerprintMode: "fast",
     incrementalFailurePolicy: "preserve-last-good",
     hybridTextScanLimit: 5_000,

package/dist/defaults.js.map

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package/dist/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../src/doctor.ts"],"names":[],"mappings":"AA4BA,OAAO,KAAK,EAAE,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,YAAY,CAAA;AAErE,wBAAsB,MAAM,CAC1B,GAAG,SAAgB,EACnB,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC,YAAY,CAAC,CAKvB;AAED,wBAAsB,gBAAgB,CACpC,MAAM,EAAE,MAAM,EACd,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC,YAAY,CAAC,CAsKvB"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../src/doctor.ts"],"names":[],"mappings":"AA8BA,OAAO,KAAK,EAAE,MAAM,EAAE,aAAa,EAAE,YAAY,EAA4B,MAAM,YAAY,CAAA;AAE/F,wBAAsB,MAAM,CAC1B,GAAG,SAAgB,EACnB,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC,YAAY,CAAC,CAKvB;AAED,wBAAsB,gBAAgB,CACpC,MAAM,EAAE,MAAM,EACd,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC,YAAY,CAAC,CA0KvB"}

package/dist/doctor.js

@@ -1,5 +1,6 @@
 import { existsSync } from "node:fs";
 import path from "node:path";
+import { noiseFloorAdvice } from "./abstention-calibration.js";
 import { findProjectConfig, loadConfig, projectConfigExists, readMergedProjectConfig, retrievalProfileOverrides, } from "./config.js";
 import { RAGMIR_DIR } from "./defaults.js";
 import { countSkippedByReason } from "./files.js";
@@ -13,6 +14,7 @@ import { isCompatibleQualityReport } from "./quality-report.js";
 import { runtimeInfo } from "./runtime-info.js";
 import { securityAuditWithConfig } from "./security.js";
 import { AGENT_HELPER_CONFIG_FILENAMES, AGENT_SETUP_FILENAME, inspectAgentIntegration, MCP_CONFIG_FILENAME, SKILL_NAMES, } from "./skill.js";
+import { fragmentationWarning } from "./storage-maintenance.js";
 import { readIndexManifest, readIndexManifestHeader } from "./store.js";
 export async function doctor(cwd = process.cwd(), options = {}) {
     const signal = operationSignal(options);
@@ -94,6 +96,7 @@ export async function doctorWithConfig(config, options = {}) {
     const profileOverrides = initialized
         ? retrievalProfileOverrides(await readMergedProjectConfig(projectConfig).catch(() => ({})), config.retrievalProfile)
         : [];
+    const runCommand = (args) => command.display + (args.length > 0 ? ` ${args.join(" ")}` : "");
     const nextSteps = nextActions({
         initialized,
         profileOverrides: profileOverrides.map((override) => `${override.field}: ${override.configured} in the config overrides the ${config.retrievalProfile} profile's ${override.profileValue}. Remove it to follow the profile, or set retrievalProfile to "custom" to keep it deliberately.`),
@@ -120,7 +123,9 @@ export async function doctorWithConfig(config, options = {}) {
         freshnessWarning,
         lexicalIndexCurrent,
         lexicalScanWarning,
-        run: (args) => command.display + (args.length > 0 ? ` ${args.join(" ")}` : ""),
+        fragments: manifest?.maintenance?.fragments,
+        noiseFloorAdvice: noiseFloorAdvice(manifest, config, runCommand),
+        run: runCommand,
     });
     throwIfAborted(signal);
     return {
@@ -195,7 +200,11 @@ function nextActions(input) {
         steps.push(`${input.noncanonicalPaths} indexed path(s) use decomposed Unicode names from an older release. Run \`${input.run(["ingest"])}\` once to store canonical paths that path filters and citations match on every platform.`);
     }
     if (input.chunksIndexed === 0 || input.missingFromIndex > 0 || input.staleInIndex > 0) {
-        steps.push(`Run \`${input.run(["doctor", "--fix"])}\` to rebuild stale or missing index data.`);
+        // Setup, repair, and upgrade never ingest on their own while a security warning stands, such as
+        // configured external extractors: only an explicit ingest runs those commands.
+        steps.push(input.warnings > 0
+            ? `Run \`${input.run(["ingest"])}\` to index stale or missing files. \`doctor --fix\` and \`upgrade\` do not ingest while a security warning stands, such as configured external extractors.`
+            : `Run \`${input.run(["doctor", "--fix"])}\` to rebuild stale or missing index data.`);
         steps.push(`Run \`${input.run(["audit"])}\` to verify missingFromIndex=0 and staleInIndex=0.`);
         if (input.chunksIndexed > 0) {
             steps.push(`Run \`${input.run(["hooks", "install"])}\` to refresh the index automatically after commits, merges, and checkouts.`);
@@ -211,6 +220,13 @@ function nextActions(input) {
     if (input.lexicalScanWarning) {
         steps.push(input.lexicalScanWarning);
     }
+    const storageWarning = fragmentationWarning(input.fragments, input.run);
+    if (storageWarning) {
+        steps.push(storageWarning);
+    }
+    if (input.noiseFloorAdvice) {
+        steps.push(input.noiseFloorAdvice);
+    }
     if (input.concentrationWarning) {
         steps.push(input.concentrationWarning);
     }